Error after Clustering completes

[HoxB8]

Hello,

I tried to cluster 31 files using the GUI with UMAP and TSNE and k=18. It appears to cluster fine and then the shiny app would crash. It appears the problem is in the step of writing and saving the file. Of note, this error didn't happen when I try to cluster 8 files. Is this something that happens with many files. Please see below for the error.

I appreciate any help.

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Input arguments:

• Project Name:
  teset

• Input FCS files for analysis:

  -BM_Group1_3944_IgG_BM.fcs
  -BM_Group1_3945_IgG_BM.fcs
  -BM_Group1_3946_IgG_BM.fcs
  -BM_Group1_3947_IgG_BM.fcs
  -BM_Group1_3951_aLy6G_BM.fcs
  -BM_Group1_3952_aLy6G_BM.fcs
  -BM_Group1_3953_aLy6G_BM.fcs
  -BM_Group1_3954_aLy6G_BM.fcs
  -LV_Group1_3944_IgG_LV.fcs
  -LV_Group1_3945_IgG_LV.fcs
  -LV_Group1_3946_IgG_LV.fcs
  -LV_Group1_3947_IgG_LV.fcs
  -LV_Group1_3951_aLy6G_LV.fcs
  -LV_Group1_3952_aLy6G_LV.fcs
  -LV_Group1_3953_aLy6G_LV.fcs
  -LV_Group1_3954_aLy6G_LV.fcs
  -PB_Group1_3944_IgG_PB.fcs
  -PB_Group1_3946_IgG_PB.fcs
  -PB_Group1_3947_IgG_PB..fcs
  -PB_Group1_3951_aLy6G_PB..fcs
  -PB_Group1_3952_aLy6G_PB.fcs
  -PB_Group1_3953_aLy6G_PB.fcs
  -PB_Group1_3954_aLy6G_PB.fcs
  -SP_Group1_3944_IgG_SP.fcs
  -SP_Group1_3945_IgG_SP.fcs
  -SP_Group1_3946_IgG_SP.fcs
  -SP_Group1_3947_IgG_SP.fcs
  -SP_Group1_3951_aLy6G_SP.fcs
  -SP_Group1_3952_aLy6G_SP.fcs
  -SP_Group1_3953_aLy6G_SP.fcs
  -SP_Group1_3954_aLy6G_SP.fcs

• Markers:

  -160Dy<160Dy_SIRPa>
  -161Dy<161Dy_CXCR2>
  -162Dy<162Dy_SiglecF>
  -163Dy<163Dy_CX3CR1>
  -164Dy<164Dy_CD27>
  -165Ho<165Ho_CCR2>
  -166Er<166Er_FcER1a>
  -167Er<167Er_CD84>
  -168Er<168Er_NK1.1>
  -170Er<170Er_cKit>
  -Yb171Di<171Yb_CD62L>
  -Yb172Di<172Yb_TCRgd>
  -Yb173Di<173Yb_CD64>
  -Yb174Di<174Yb_IgM>
  -Lu175Di<175Lu_CD44>
  -Yb176Di<176Yb_F480>
  -113In<113In_Ter119>
  -115In<115In_CD45>
  -La139Di<139La_MHCII>
  -140Ce<140Ce_IgD>
  -Pr141Di<141Pr_B220>
  -Nd142Di<142Nd_CD49b>
  -Nd143Di<143Nd_CD11c>
  -Nd144Di<144Nd_CD206>
  -Nd145Di<145Nd_CD80>
  -Nd146Di<146Nd_PD-1>
  -Sm147Di<147Sm_PD-L1>
  -Nd148Di<148Nd_PDCA1>
  -Sm149Di<149Sm_CD124>
  -Nd150Di<150Nd_CD86>
  -151Eu<151Eu_Ly6C>
  -Sm152Di<152Sm_Ly6B>
  -153Eu<153Eu_CD11b>
  -Sm154Di<154Sm_CD115>
  -155Gd<155Gd_CD8>
  -156Gd<156Gd_CD4>
  -157Gd<157Gd_CD3>
  -Tb159Di<159Tb_CD101>

• Data merging method:
  ceil

• Data transformation method:
  arcsinh

• Dimensionality reduction method:
  tsne

• Data clustering method(s):
  Rphenograph

• Data visualization method(s):
  tsneumap

• Subset progression analysis method:
  NULL

Extract expression data...
232500 x 41 data was extracted!

Dimension reduction...
Running t-SNE...with seed42
DONE

Running UMAP...with seed42
DONE

Run clustering...
Running PhenoGraph...
Run Rphenograph starts:
-Input data of 232500 rows and 38 columns
-k is set to 18
Finding nearest neighbors...
DONE ~1853.17000000001s
Compute jaccard coefficient between nearest-neighbor sets...
DONE ~17.8600000000006s
Build undirected graph from the weighted links...
DONE ~11.2200000000012s
Run louvain clustering on the graph ...
DONE ~28.8600000000006s

Run Rphenograph DONE, took a total of 1911.11000000001s.
Return a community class
-Modularity value:0.906624079042367

-Number of clusters:45
DONE!

Progression analysis...
Listing markers used for dimension reduction...
Stashing sample names...
Wrapping results...
Analysis DONE, saving the results...
R object is saved in teset.RData

THIS R OBJECT IS THE INPUT OF SHINY APP!
Warning: Removed 37500 rows containing missing values (geom_point).
12: execCallbacks(timeoutSecs, all, loop$id)
11: run_now(timeoutMs/1000, all = FALSE)
10: service(timeout)
9: serviceApp()
8: ..stacktracefloor..(serviceApp())
7: withCallingHandlers(expr, error = doCaptureStack)
6: domain$wrapSync(expr)
5: promises::with_promise_domain(createStackTracePromiseDomain(),
expr)
4: captureStackTraces({
while (!.globals$stopped) {
..stacktracefloor..(serviceApp())
}
})
3: ..stacktraceoff..(captureStackTraces({
while (!.globals$stopped) {
..stacktracefloor..(serviceApp())
}
}))
2: shiny::runApp(system.file("shiny", package = "cytofkit2"), host = host)
1: cytofkit_shiny_dashboard()
Warning: Error in if: missing value where TRUE/FALSE needed
2: shiny::runApp
1: cytofkit_shiny_dashboard